• Density plots
  • " />
    suppressPackageStartupMessages({
      library("SummarizedExperiment")
      library("magrittr")
      library("plotlyutils")
      library("plotly")
      library("limma")
    })
    • TCGA Glioblastoma (GBM) data
    • 5,000 randomly chosen genes, plus a gene signature (mentioned in vignette G)
    mat <- assay(GBMdata) + 0.5
    # ind <- sample(1:ncol(mat), 30)
    plotly_density(
        log2(mat), 
        palette=colorspace::rainbow_hcl,
        xlab = "log<sub>2</sub>(reads + 0.5)") %>% 
        layout(showlegend = FALSE)
    plotly_density(
        voomed_GBM$E, 
        palette=colorspace::rainbow_hcl,
        xlab = "log<sub>2</sub>(normalised counts per million)") %>%
        layout(showlegend = FALSE)